Complete Chloroplast Genome of Nepeta griffithii and Comparative Genomics of 10 Nepeta Species
5 affiliations
- 1State Key Laboratory of Chinese Medicine Modernization Tianjin University of Traditional Chinese Medicine Tianjin China
- 2Haihe Laboratory of Modern Chinese Medicine Tianjin China
- 3Department of Biotechnology National University of Medical Sciences Rawalpindi Pakistan
- 4State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing P. R. China
- 5Institute of Traditional and Alternative Medicine (ITAM) University of Health and Allied Sciences (UHAS) Ho Ghana
Abstract
Nepeta L. (Lamiaceae) is an ecologically and medicinally important genus, yet complete cp genome resources are available for fewer than 10 of the approximately 300 accepted species, with western Himalayan taxa almost entirely unrepresented. Here, we sequenced, assembled, and annotated the complete cp genome of Nepeta griffithii and compared it with nine previously published Nepeta cp genomes. The 10 cp genomes exhibited a highly conserved quadripartite structure, with genome sizes ranging from 151,254 to 152,348 bp, and contained 113 unique genes (79 protein‐coding, 30 tRNA, 4 rRNA). Gene content, guanine‐cytosine content, intron features, and inverted repeat contraction and expansion were highly conserved. SSR analysis identified 387 repeats across the 10 cp genomes, predominantly mononucleotide A/T motifs in intergenic spacers, yielding candidate cpSSR markers for population‐level studies. Codon usage analysis revealed a strong bias toward A/T‐ending codons, with leucine as the most frequent amino acid. Nucleotide diversity analysis showed intergenic spacers were more variable than both introns and genic regions. Highly polymorphic loci, including ccsA‐ndhD, rpl32‐trnL‐UAG, and ndhG‐ndhI, were identified as candidate markers for phylogenetic and population studies. Maximum likelihood phylogeny based on 79 concatenated protein‐coding genes recovered a well‐resolved topology within Nepeta and placed N. griffithii as sister to N. nuda with maximal bootstrap support of 100%. This study provides the first complete cp genome for N. griffithii, improves plastome sampling within the genus, and offers genomic markers for species identification, systematics, and evolutionary studies.
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BibTeX
@article{li2026complete,
title = {{Complete Chloroplast Genome of Nepeta griffithii and Comparative Genomics of 10 Nepeta Species}},
author = {Xinyi Li and Abdul Sammad and Sayed Afzal Shah and Jiahui Sun and Aman Karim and Bartholomew Yir‐erong and Xiaoxuan Tian and Abdullah},
journal = {Ecology and Evolution},
year = {2026},
month = oct,
doi = {10.1002/ece3.74582},
url = {https://doi.org/10.1002/ece3.74582},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Complete Chloroplast Genome of Nepeta griffithii and Comparative Genomics of 10 Nepeta Species
AU - Xinyi Li
AU - Abdul Sammad
AU - Sayed Afzal Shah
AU - Jiahui Sun
AU - Aman Karim
AU - Bartholomew Yir‐erong
AU - Xiaoxuan Tian
AU - Abdullah
PY - 2026
DA - 2026/10/01
JO - Ecology and Evolution
DO - 10.1002/ece3.74582
UR - https://doi.org/10.1002/ece3.74582
AB - Nepeta L. (Lamiaceae) is an ecologically and medicinally important genus, yet complete cp genome resources are available for fewer than 10 of the approximately 300 accepted species, with western Himalayan taxa almost entirely unrepresented. Here, we sequenced, assembled, and annotated the complete cp genome of Nepeta griffithii and compared it with nine previously published Nepeta cp genomes. The 10 cp genomes exhibited a highly conserved quadripartite structure, with genome sizes ranging from 151,254 to 152,348 bp, and contained 113 unique genes (79 protein‐coding, 30 tRNA, 4 rRNA). Gene content, guanine‐cytosine content, intron features, and inverted repeat contraction and expansion were highly conserved. SSR analysis identified 387 repeats across the 10 cp genomes, predominantly mononucleotide A/T motifs in intergenic spacers, yielding candidate cpSSR markers for population‐level studies. Codon usage analysis revealed a strong bias toward A/T‐ending codons, with leucine as the most frequent amino acid. Nucleotide diversity analysis showed intergenic spacers were more variable than both introns and genic regions. Highly polymorphic loci, including ccsA‐ndhD, rpl32‐trnL‐UAG, and ndhG‐ndhI, were identified as candidate markers for phylogenetic and population studies. Maximum likelihood phylogeny based on 79 concatenated protein‐coding genes recovered a well‐resolved topology within Nepeta and placed N. griffithii as sister to N. nuda with maximal bootstrap support of 100%. This study provides the first complete cp genome for N. griffithii, improves plastome sampling within the genus, and offers genomic markers for species identification, systematics, and evolutionary studies.
SN - 2045-7758
ER -